Zotero: Citation Management Tool: ZotFile

ZotFile is a third-party plug-in that allows you to add highlights and annotations to PDFs saved to your Zotero Library and extract those to notes attached to your citations. 

To install:

1. On the ZotFile site, click Download and the xpi file will be downloaded. 
2. In the Zotero application, go to Tools > Add-Ons.
3. Click on the gear icon and choose "Install Add-on from file"
4. Locate your downloaded xpi file and click Open

When you open a PDF in your Zotero library with an application that adds highlights and annotations, Zotero can extract these and save them as attached notes in Zotero. 

In this document I have highlighted some text and added a comment. In my Zotero library I right-click on the PDF and choose "Manage Attachments," then "Extract Annotations."

The highlighted section and my comment are added as a note and attached to the citation. ZotFile also includes the page number of the highlighted text. The link allows me to quickly return to that section of the PDF. 

An alternative to syncing files using Zotero's or a WebDAV server is to use ZotFile along with a cloud storage service, such as Google Drive, Dropbox, Box, MEGA, or Sync. Your first step is to choose a service and download its desktop sync app. (In this example, I am using Box.) In the syncing folder for the cloud storage service, create a new folder where your PDFs will be stored. Before proceeding, in Zotero go to Edit > Preferences > Sync and uncheck "Sync attachment files in My Library...".

Go to Zotero Tools > ZotFile preferences > General Settings. Set the Source Folder for Attaching New Files to a desired folder (usually your Downloads folder). This is the folder ZotFile will look to when you right-click on a Zotero reference and select "Add attachment from source folder."  You will rarely use this if you've already configured Zotero to automatically download the PDF any time you create a reference from the browser connector (Edit > Preferences > General).

Set Location of Files to "Custom Location" and point it to the folder you created in your cloud syncing app.

Leaving "Use subfolder defined by" unchecked will store all your PDFs in a single folder on the sync drive. There are directions on the ZotFile site for organizing your PDFs into subfolders.

Under Advanced Settings, check "Remove special characters (diacritics) from filename."

If you plan to sync across multiple devices, in Zotero you will need to set up relative paths in the "Linked Attachment Base Directory." Go to Zotero preferences > Advanced > Files and Folders and set Linked Attachment Base Directory to the folder you created in your cloud syncing app. You will have to do this on each of the computers on which you want to access the files.

To move files already attached to citations in your Zotero library, sort your library on the attachments column.

[Before taking the next step, you may want to back up your attachments by copying the storage folder from the Zotero directory on your computer.]

Select all the items with attachments, right-click on the selected files, and choose Manage Attachments > Rename Attachments. ZotFile will move the files from the storage folder in your Zotero directory to the folder specified in the preferences. In the Zotero library, you will now see attached links to the files in this folder.

Now when using the Zotero connector to save a reference to your library, the attached file will be saved to the folder you created in your sync app and a link to that file will be attached to the reference in the library. To annotate the attachments, use the link to open a PDF, annotate and save it, then right-click on the link and choose Manage Attachments > Extract Annotations. 

Note: Because the PDFs are now stored outside of the Zotero directory, moving items to the trash will only delete the reference, not the PDF. Follow these steps:

1. Right-click on the link to the attachment and choose "Show File." This opens up your storage folder where you can delete the PDF.
2. In Zotero, right-click on the reference and select "Move Item to Trash" (or type Ctrl+Delete).

In your Zotero preferences (under General) one default option is to automatically attach PDFs when saving items to your Library. The attachments will often have some generic title as shown in the image below. 

If you right-click on the file, you have the option to "Rename File From Parent Metadata." With ZotFile, that renaming process happens automatically when an attached file is added to your Zotero library.  

In preparation for sharing PDFs between your Zotero library and your tablet, you must install an app on your computer and tablet that will allow you to sync files between them. Dropbox is used in the example here. 

In Tools > ZotFile Preferences > General Settings, choose the folder that syncs with your 

In Tools > ZotFile Preferences > Tablet Setting, specify a directory that you have created in your Dropbox folder on your computer. Check the boxes indicated in the image. Files that are copied to your folder should automatically appear in your PDF reader application (you may need to give the application permission to access the folder).

Right-click on a PDF in Zotero and choose Manage Attachments > Send to Tablet. If you annotate that document, you can add the annotated version to your Zotero library by choosing Manage Attachments > Get from Tablet. A PDF with the suffix "_annotated" will be added to your library and any annotations will be added as notes.